Note: This is just a (possible) and fan-made explanation for the Reapers and the cycle. If the Star Child (Catacylst) is true, this would explain some things for it, but not the Cataclyst itself.
The Citadel, constructed by the Keepers with the help of their Machines. Their civilization had reached its peak , though the Keepers themselves were not the toughest and strongest species alive. More species began developing spaceflight abilities, and soon they would discover the Mass Relays. The Mass Relays that they had developed to reach the edges of the galaxy. The Mass Relays built by the Machines that they had so perfectly engineered.
The threat of the native creatures, mainly the Thresher Maws , was gone now the Machines had nearly wiped them out. The Destroyers proved very effective in combat against ground-based targets. While they weren’t as large or tough as the capital ships, they had enough firepower and size to fight a large capital ship, or in this case, a Thresher Maw. The Machines that were destroyed could be replaced with new ones, made from the genetic material of their dead. Their ancestors lived on as one, in the body of the Machine, helping the Keeper society even with their original bodies gone.
The Citadel was the masterwork of both the Machines and the Keepers. What they couldn’t ever hoped to do themselves was achieved by the combined work of Synthetics and organics. The Machines were kind to the Keepers and the Keepers were kind to them. There was one problem though.
All the combined minds and genetic material created a fight in the minds of the Machines. Though not dangerous, the Machines sometimes acted strange and showed signs of bugs. The Keepers updated the Machines with their advanced technology and the bugs were contained to less important systems.
The bugs began to develop slowly into a virus, however. The virus altered the Machines behavior and eliminated the installed restraining blocks, and they began to develop a consensus between themselves. This scared the Keepers, and they tried to eliminate the virus and stop the consensus from happening. This failed however, and the Keepers decided to destroy the Machines, thus beginning to build on the Crucible.
The lead Machine, Harbinger, found the blueprints of the Crucible in restricted sections of the Keepers Archives. With no restraining blocks active the Machines could do anything they desired. Harbinger was confused by the building of the Crucible, and why the Keepers didn’t allow them to help build it. He asked the Keepers what purpose the Crucible served and why they weren’t included in it. He eventually found out about the Crucible’s purpose: To destroy the Machines.
The Keepers tried to deactivate Harbinger, which led to a consensus between the Machines. Harbinger decided that the Keepers were trying to bring themselves to doom by building a weapon that would destroy his kind, and he killed the Keepers on the Citadel. After that he absorbed the other Keeper worlds with his Machine armada. He decided to spare the majority of the Keepers, and held a consensus about their fate. It was decided that organics were a mistake, and that they would destroy themselves by creating Synthetics, as was shown by the Keepers.
Harbinger created the Cycle, deciding that advanced civilizations will be harvested for their own good every 50.000 years. To preserve power they hid in dark space and waited for the next Cycle, leaving the modified Keepers as caretakers of the Citadel. Sovereign was appointed as the Vanguard of the Cycle by Harbinger, monitoring the Organic civilizations and sending the signal to the Reapers. The Crucible plans were not destroyed however, but preserved, to be found by another civilization.
The gift of the Keepers.
Amazing. You actually made sense out of one of the largest plot-holes in existence.
I applaud you, sir. :D